some question about programming epcs

In my new work ,I have to design a FPGA system, when the product is assembled,the JTAG interface is unavailable. After some experiment, I need to update some parameters in the system ,but now I can't disassemble the product because the disassembly may change the parameters that I have gotten,so I can't program the epcs through JTAG.

While, my question is coming.Whether can I update the config data of FPGA or nios software image that storage in EPCS through some interface to PC,such as UART,USB?

For example,I have a UART to pc always active,when the system power on, a specifical circult in FPGA will receive something from PC through UART ,if it receives a update command ,it will receive config data from pc and send them to EPCS. or FPGA will implement the normal program.

please help,thank you!